deploy: 88449ed

Introduction.html

@@ -414,6 +414,8 @@ <h2> Contents </h2>
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-goals">Learning Goals</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#getting-started">Getting Started</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#principles-of-mri-course-lectures">Principles of MRI Course Lectures</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#using-mri-education-resources-code">Using MRI-Education-Resources code</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#acknowledgements">Acknowledgements</a></li>
 </ul>
             </nav>
@@ -450,18 +452,24 @@ <h2>Learning Goals<a class="headerlink" href="#learning-goals" title="Permalink
 <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this heading">#</a></h2>
 <p>This book jumps pretty quickly into concepts, for a quick overview of MRI, here’s my attempt to explain MRI in under 10 minutes:</p>
 <p><a class="reference external" href="https://youtu.be/1Ku6-uXw7Ag">How MRI Works (Explained In under 10 minutes)</a></p>
+</section>
+<section id="principles-of-mri-course-lectures">
+<h2>Principles of MRI Course Lectures<a class="headerlink" href="#principles-of-mri-course-lectures" title="Permalink to this heading">#</a></h2>
 <p>You can also access a full playlist of my lectures</p>
 <p><a class="reference external" href="https://www.youtube.com/playlist?list=PLjBt5Iq93BT9eXMsgevVTXKVv4BgVLB1X">Principles of MRI Recorded Lectures</a></p>
 </section>
+<section id="using-mri-education-resources-code">
+<h2>Using MRI-Education-Resources code<a class="headerlink" href="#using-mri-education-resources-code" title="Permalink to this heading">#</a></h2>
+<p>If you would like to use the associated code that goes along with this book, it is available at the git repository <a class="github reference external" href="https://github.com/LarsonLab/MRI-education-resources">LarsonLab/MRI-education-resources</a>, and also the GitHub icon above.  I recommend cloning the repository via the GitHub Desktop application, this way you get all the code at once and then can pull any updates made to the repository.</p>
+</section>
 <section id="acknowledgements">
 <h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this heading">#</a></h2>
 <p>This book is greatly influenced by many other great resources that I want to acknowledge up front:</p>
 <ul class="simple">
 <li><p><em>Principles of Magnetic Resonance Imaging</em> by Dwight Nishimura - I learned from this great text and borrowed a lot of its material.  For some of my students with less engineering/signal processing background, this book on its own was challenging.</p></li>
 <li><p>Net magnetizations animation from Bill Overall and the <a class="reference external" href="https://vista.ai/products/research-spinbench/">SpinBench</a> simulation and pulse sequence design tool</p></li>
 <li><p>Miki Lustig’s MRI course notes</p></li>
-<li><p>Educational resources from the <a class="reference external" href="https://www.drcmr.dk/MR">Danish Research Centre for Magnetic Resonance</a>, which includes a great on-line [Bloch Simulation]
-(<a class="reference external" href="http://drcmr.dk/BlochSimulator/">http://drcmr.dk/BlochSimulator/</a>)</p></li>
+<li><p>Educational resources from the <a class="reference external" href="https://www.drcmr.dk/MR">Danish Research Centre for Magnetic Resonance</a>, which includes a great on-line <a class="reference external" href="http://drcmr.dk/BlochSimulator/">Bloch Simulator</a></p></li>
 </ul>
 </section>
 <div class="toctree-wrapper compound">
@@ -536,6 +544,8 @@ <h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permal
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-goals">Learning Goals</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#getting-started">Getting Started</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#principles-of-mri-course-lectures">Principles of MRI Course Lectures</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#using-mri-education-resources-code">Using MRI-Education-Resources code</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#acknowledgements">Acknowledgements</a></li>
 </ul>
   </nav></div>

Spatial Encoding.html

@@ -589,10 +589,10 @@ <h3>Frequency Encoding<a class="headerlink" href="#frequency-encoding" title="Pe
 </pre></div>
 </div>
 <img alt="_images/77cfcd054449f55c4465bccad72f41e206eb0861f80630d348f6a70d7eb54681.png" src="_images/77cfcd054449f55c4465bccad72f41e206eb0861f80630d348f6a70d7eb54681.png" />
-<img alt="_images/aa622fa30e442abad38f8adbf513e8f8afc703d56338cb1620ca3acd0ebe30ab.png" src="_images/aa622fa30e442abad38f8adbf513e8f8afc703d56338cb1620ca3acd0ebe30ab.png" />
 <img alt="_images/ee9681136c56b2b7a3abc0065df5a7c4465b4d0c3564bb93bcbfcdb805e76a81.png" src="_images/ee9681136c56b2b7a3abc0065df5a7c4465b4d0c3564bb93bcbfcdb805e76a81.png" />
 <img alt="_images/94f0bb94ef66078a0702a9a60652e1592422b13023ec17d8caf206975519be25.png" src="_images/94f0bb94ef66078a0702a9a60652e1592422b13023ec17d8caf206975519be25.png" />
 <img alt="_images/eacaff314d6ca100a1babd6711c2a3ebefa7a000b233cd854414a16ddfcf76f8.png" src="_images/eacaff314d6ca100a1babd6711c2a3ebefa7a000b233cd854414a16ddfcf76f8.png" />
+<img alt="_images/aa622fa30e442abad38f8adbf513e8f8afc703d56338cb1620ca3acd0ebe30ab.png" src="_images/aa622fa30e442abad38f8adbf513e8f8afc703d56338cb1620ca3acd0ebe30ab.png" />
 <img alt="_images/633fd62680141f067fd0027944b5856b7f36825f6b9614c7852ef6dc936df389.png" src="_images/633fd62680141f067fd0027944b5856b7f36825f6b9614c7852ef6dc936df389.png" />
 </div>
 </div>
@@ -648,14 +648,14 @@ <h2>Phase Encoding<a class="headerlink" href="#phase-encoding" title="Permalink
 </div>
 <div class="cell_output docutils container">
 <img alt="_images/011e2056fd0c8fbb0da3c4e71a79966c2eee21e53b758099e3d05cd0014d4d84.png" src="_images/011e2056fd0c8fbb0da3c4e71a79966c2eee21e53b758099e3d05cd0014d4d84.png" />
-<img alt="_images/5e937688aa6f798671b70d6a4466fa2c6a099ee18dfb22ac3d920559cacd6cf6.png" src="_images/5e937688aa6f798671b70d6a4466fa2c6a099ee18dfb22ac3d920559cacd6cf6.png" />
-<img alt="_images/d479e33cd40c7e8f050b885cfc7516482374b52d7e1e07a4de34632ef4da98a4.png" src="_images/d479e33cd40c7e8f050b885cfc7516482374b52d7e1e07a4de34632ef4da98a4.png" />
 <img alt="_images/32efafd44f9c42012b9e052358871df664cdf95eb347386f28f8355d2367511f.png" src="_images/32efafd44f9c42012b9e052358871df664cdf95eb347386f28f8355d2367511f.png" />
+<img alt="_images/5e937688aa6f798671b70d6a4466fa2c6a099ee18dfb22ac3d920559cacd6cf6.png" src="_images/5e937688aa6f798671b70d6a4466fa2c6a099ee18dfb22ac3d920559cacd6cf6.png" />
 <img alt="_images/d70e301f75685957891808a298dc6593fb63e3e55c93ea5d37ae1cf4ed3bf08c.png" src="_images/d70e301f75685957891808a298dc6593fb63e3e55c93ea5d37ae1cf4ed3bf08c.png" />
 <img alt="_images/1be703ba81b8a1b721b93d9c7830be74efab2fcacfef101ad876a2f4dbaa1dca.png" src="_images/1be703ba81b8a1b721b93d9c7830be74efab2fcacfef101ad876a2f4dbaa1dca.png" />
-<img alt="_images/75a393e1f5c9b0c7948db12f3e0b9837e16a90bdd7ec0c51b50bdbea904b5f3b.png" src="_images/75a393e1f5c9b0c7948db12f3e0b9837e16a90bdd7ec0c51b50bdbea904b5f3b.png" />
 <img alt="_images/d3a7f0e6540bcb26db8b0480477d2511c249b42c8bfbf38f211e058c1e758e83.png" src="_images/d3a7f0e6540bcb26db8b0480477d2511c249b42c8bfbf38f211e058c1e758e83.png" />
 <img alt="_images/5dc4c6c9a59278cc0856faed17f29d353f5de24f614498aecac1ae37bd6d7ef2.png" src="_images/5dc4c6c9a59278cc0856faed17f29d353f5de24f614498aecac1ae37bd6d7ef2.png" />
+<img alt="_images/d479e33cd40c7e8f050b885cfc7516482374b52d7e1e07a4de34632ef4da98a4.png" src="_images/d479e33cd40c7e8f050b885cfc7516482374b52d7e1e07a4de34632ef4da98a4.png" />
+<img alt="_images/75a393e1f5c9b0c7948db12f3e0b9837e16a90bdd7ec0c51b50bdbea904b5f3b.png" src="_images/75a393e1f5c9b0c7948db12f3e0b9837e16a90bdd7ec0c51b50bdbea904b5f3b.png" />
 </div>
 </div>
 </section>

_sources/Introduction.md

@@ -26,17 +26,22 @@ This book jumps pretty quickly into concepts, for a quick overview of MRI, here'
 
 [How MRI Works (Explained In under 10 minutes)](https://youtu.be/1Ku6-uXw7Ag)
 
+## Principles of MRI Course Lectures
+
 You can also access a full playlist of my lectures
 
 [Principles of MRI Recorded Lectures](https://www.youtube.com/playlist?list=PLjBt5Iq93BT9eXMsgevVTXKVv4BgVLB1X)
 
+## Using MRI-Education-Resources code
+
+If you would like to use the associated code that goes along with this book, it is available at the git repository https://github.com/LarsonLab/MRI-education-resources, and also the GitHub icon above.  I recommend cloning the repository via the GitHub Desktop application, this way you get all the code at once and then can pull any updates made to the repository.
+
 ## Acknowledgements
 
 This book is greatly influenced by many other great resources that I want to acknowledge up front:
 
 * _Principles of Magnetic Resonance Imaging_ by Dwight Nishimura - I learned from this great text and borrowed a lot of its material.  For some of my students with less engineering/signal processing background, this book on its own was challenging.
 * Net magnetizations animation from Bill Overall and the [SpinBench](https://vista.ai/products/research-spinbench/) simulation and pulse sequence design tool
 * Miki Lustig's MRI course notes
-* Educational resources from the [Danish Research Centre for Magnetic Resonance](https://www.drcmr.dk/MR), which includes a great on-line [Bloch Simulation]
-(http://drcmr.dk/BlochSimulator/)
+* Educational resources from the [Danish Research Centre for Magnetic Resonance](https://www.drcmr.dk/MR), which includes a great on-line [Bloch Simulator](http://drcmr.dk/BlochSimulator/)
 

reports/FOV and Resolution.err.log

@@ -3,7 +3,7 @@ Traceback (most recent call last):
     executenb(
   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 1305, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 173, in wrapped
+  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
     return loop.run_until_complete(inner)
   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
     return future.result()

reports/Image Reconstruction.err.log

@@ -1,9 +1,9 @@
 Traceback (most recent call last):
   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 778, in _async_poll_for_reply
     msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
-  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 189, in ensure_async
+  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 198, in ensure_async
     result = await obj
-  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_client/channels.py", line 315, in get_msg
+  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_client/channels.py", line 313, in get_msg
     raise Empty
 _queue.Empty
 
@@ -14,7 +14,7 @@ Traceback (most recent call last):
     executenb(
   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 1305, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 173, in wrapped
+  File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
     return loop.run_until_complete(inner)
   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
     return future.result()